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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagaacttttccagtttcaaccccctacatttgaatcattagaatattatggaattttcccttcaatttgaaattctaattatccatcattttacagggtttttcgtgaatagagagaacattattttacttggaacagtaatactaatggacgcgtctttttctttattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGATGGCTTATTTAAG

Basic information

species Zea mays
transcript GRMZM2G402002_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 5
gtgcagaacttttccagtttcaaccccctacatttgaatcattagaatattatggaattttcccttcaatttgaaattctaattatccatcattttacagggtttttcgtgaatagagagaacattattttacttggaacagtaatactaatggacgcgtctttttctttattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGATGGCTTATTTAAG
|||       |||||   || || | || |  || |   | |   || ||| || || |  |||||| || |  |  ||||  ||| ||  || |                 |||| ||   |||| |||| |      |  | ||| |  ||| |         |   |||  | |||||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||||| |||||||||
gtgtgtggtatttccgaattgaaactccaatgttgg---cttgtaaaaattgtgaaactaccccttctatgtaga--tcta--tatgcaatatat-----------------atag-gaatgcattcttttgcc-----ctcttatatt--tggccaa-------ttactataatgtagATTGGGATCATCGACCCTGACTGTAGACTTATTGGTCTTCACCTCTACGATGGATTATTTAAG

upper sequence: GRMZM2G402002_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 5
gtgcagaacttttccagtttcaaccccctacatttgaatcattagaatattatggaattttcccttcaat-ttgaaattctaattatccatcattttacagggtttttcgtgaatagagagaacattattttacttggaac-agtaatac-taatggacgcgtctt---tttctttattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGATGGCTTATTTAAG
                                                  |||  | |||    |    | ||   ||| |  | ||  |  | | |   || |||      | || |    | ||||||||  ||| ||| | |   || |  |   |  || ||   ||||| |  || |||||||||||| ||||| ||||| || ||| | ||||| |||||| | |||||||| |||||||||
-------------------------------------------------gtatcaattttaatttatgctctttttattttgttcatgaactactgtgttggattt----caattatactctaaattattttttttgcaaccacttggacatgttaaccatgttttaattttctcttctccatagATTGGAATTATTGATCCTGATTGCAGATTAATTGGACTTCATTTATATGATGGATTATTTAAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|74245573|gb|DT653487.1|DT653487
EST:     CCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAG                         ATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGAT
genomic: CCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAGgtgcagaact ... tattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGAT
EST: gi|32933109|gb|CF037921.1|CF037921
EST:     CCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAG                         ATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGAT
genomic: CCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAGgtgcagaact ... tattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGAT
EST: gi|78113492|gb|DV531883.1|DV531883
EST:     CCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAG                         ATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGAT
genomic: CCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAGgtgcagaact ... tattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 239

AGCCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAGgtgcagaact ... tattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGATGGCTTATTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

AGCCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAGgtgcagaact ... tattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGATGGCTTATTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

AGCCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAGgtgcagaact ... tattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGATGGCTTATTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 107

AGCCATGGGTGATGTTTCTGATCGCATTGGCCGCCCTACTGACAATGGACAGgtgcagaact ... tattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGATGGCTTATTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttacttggaacagtaatactaatggacgcgtctttttctttattctatagATTGGAATCATTGACCCTGACTGTAGACTCATTGGTCTTCATCTCTATGATGGCTTATTTAAG
                     tactaat  putative branch site (score: 107)
                                 cgtctttttctttatt  putative PPT
                                     tttttctttattctat  TA-rich tract